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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatcaccacatctttcttcttactgtttcgattgtttcttcttggttttgatttgtggggatggaaattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA

Basic information

species Arabidopsis thaliana
transcript AT5G42050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 1
----gtattcatcaccacatctttcttcttactgtttcgattgtttcttcttggttttgatttg----tggggatggaaattgttt--------------agGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
    |      | ||||    |   || |  |||| |   || || ||| ||  || | | | |    ||  |||| |  || |||              |||  |||| ||| | ||||| || || |||||| | |||||||||||  | || || ||||| ||||||||||||||||||||||| ||||| ||||  ||
atttgaggaattgaccatgcttcatttgtctctgtctt--ttcttcctttttaattctaaatcggttttgctgatgaatgtttttttttttttgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGCCCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGA

upper sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G36700.1 (Glycine max), 3'ss of exon 1
--------------gtattca-tcaccacatctttcttcttactgt-ttcgattgtttcttcttggttttgatttgtggggatggaaattgt----ttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
               | ||   | |  ||   | | | ||||   | |  ||||| | ||  ||    ||  |||    |||      ||||    |||||  |||| ||| ||||||| || || ||| | || || ||||| ||  | || || || ||||||||||| || ||||||||||||||||||||||  ||
gtttatgctgatagctgttaggtgaggacccgtgtatacttataatatctgattgatgctaattaaaattcgtttcatcggaaaatgtttgtgtttttagGTCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCTACTCACCAACTTCATGGAATCTTTGA

upper sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G02840.2 (Glycine max), 3'ss of exon 1
----------------gtattca-tcaccacatctttcttcttactgtttcgattgtttcttcttggttttgatttgtgggg--atggaaattgttt-agGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
                 | ||   | |  ||  || | | |||     |  ||||| | ||  ||   || | ||  | ||   |||    | |||| |||  |||| ||| ||||||| || || ||| | || || ||||| ||  | || || || ||||||||||| |||||||||||||| ||||||||||  ||
ttaattatactgatagctgttaggtgaggacccctgtatacttgtatatctgattgatgctaattaaattcgtttcattggaaaatgtttgtggttttagGTCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGA

upper sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------------------gtattcatca-ccacatctttcttcttactgtttcg-------attgtttcttcttggttttgatttg----tggggatggaaattgttt---------agGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
                                                                                                ||   || |     ||| ||      | || |  |       ||| || |||  |  || | | |||    ||  ||  ||  ||  ||         |||  |||| ||| ||||||| || || || ||| | |||||||||||  | ||  | ||||| ||||||||||||||||||||||| ||||| ||||  ||
gtgtgtcccctctccttttttttttcttcttgttttgctctctttatcaaatcttatttttcctttaatctaattcgcggttctctatattttcaataacaataagttgaatcctttgaggaattgatatgtcaagaaattcttcctttctaattctaaattgattttgctgacagatgtttcttgtgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGCCCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164079600|gb|ES208473.1|ES208473
EST:     TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCG                         GATTGCCACCAAGA
genomic: TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCGgtattcatca ... aattgtttagGATTGCCACCAAGA
EST: gi|164163022|gb|ES084962.1|ES084962
EST:     TCTGCAACAACGTATTACCATGGAAGAGAATCTCAAACGCCAGCTTTTCG                         GATTGCCACCAAGATACAGGGACTCGGTTAGAGCGAT
genomic: TCTGCAACAACG-A-TACCATGGAAGAGAATCTCAAACGCCAGCTTTTCGgtattcatca ... aattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGAT
EST: gi|125317126|gb|EL331211.1|EL331211
EST:     TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCG                         GATTGCCACCAAGATACAGGGACTCGGTTAGAGCG
genomic: TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCGgtattcatca ... aattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCG
EST: gi|116481291|gb|EG523883.1|EG523883
EST:     TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCG                         GATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTC
genomic: TGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCGgtattcatca ... aattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgtttcgattgtttcttcttggttttgatttgtggggatggaaattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
                                            aaattgttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcatcaccacatctttcttcttactgtttcgattgtttcttcttggttttgatttgtggggatggaaattgtttagGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA